Selected Publications

 Search for the complete list of publications in PubMed.


Tet2 Rescues Age-Related Regenerative Decline and Enhances Cognitive Function in the Adult Mouse Brain.

Gontier G, Iyer M, Shea JM, Bieri G, Wheatley EG, Ramalho-Santos M, Villeda SA.

Cell Rep. 2018 Feb 20;22(8):1974-1981. doi: 10.1016/j.celrep.2018.02.001.



Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b.

Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M.

Epigenetics Chromatin. 2017 Jul 12;10:36. doi: 10.1186/s13072-017-0143-3.


Global Hypertranscription in the Mouse Embryonic Germline.

Percharde M, Wong P, Ramalho-Santos M.

Cell Rep. 2017 Jun 6;19(10):1987-1996. doi: 10.1016/j.celrep.2017.05.036.


CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair.

Shenoy TR, Boysen G, Wang MY, Xu QZ, Guo W, Koh FM, Wang C, Zhang LZ, Wang Y, Gil V, Aziz S, Christova R, Rodrigues DN, Crespo M, Rescigno P, Tunariu N, Riisnaes R, Zafeiriou Z, Flohr P, Yuan W, Knight E, Swain A, Ramalho-Santos M, Xu DY, de Bono J, Wu H.

Ann Oncol. 2017 Jul 1;28(7):1495-1507. doi: 10.1093/annonc/mdx165.


Hypertranscription in Development, Stem Cells, and Regeneration.

Percharde M, Bulut-Karslioglu A, Ramalho-Santos M.

Dev Cell. 2017 Jan 9;40(1):9-21. doi: 10.1016/j.devcel.2016.11.010. 



Inhibition of mTOR induces a paused pluripotent state.

Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M.

Nature. 2016 Dec 1;540(7631):119-123.


YAP Induces Human Naive Pluripotency.

Qin H, Hejna M, Liu Y, Percharde M, Wossidlo M, Blouin L, Durruthy-Durruthy J, Wong P, Qi Z, Yu J, Qi LS, Sebastiano V, Song JS, Ramalho-Santos M.

Cell Rep. 2016 Mar 15;14(10):2301-12.



Unwind and transcribe: chromatin reprogramming in the early embryo.

Biechele S, Lin CJ, Rinaudo PF, Ramalho-Santos M.

Curr Opin Genet Dev2015 Jul 13;34:17-23.


Emergence of hematopoietic stem and progenitor cells involves a Chd1-dependent increase in total nascent transcription.

Koh FM, Lizama CO, Wong P, Hawkins JS, Zovein AC, Ramalho-Santos M.

Proc Natl Acad Sci USA. 2015 Apr 7;112(14):E1734-43


Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast.

Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M.

Development. 2015 Jan 1;142(1):118-27



HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.

Diaz AA, Qin H, Ramalho-Santos M, Song JS.

Nucleic Acids Res. 2014 Nov 26


A comparative encyclopedia of DNA elements in the mouse genome.

Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64


Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote.

Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M.

Dev Cell. 2014 Aug 11;30(3):268-79.

Systematic Identification of Barriers to Human iPSC Generation.
Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M.
Cell. 2014 Jul 17;158(2):449-61.



Histone variant H3.3 maintains a decondensed chromatin state essential for mouse preimplantation development. 
Lin CJ, Conti M, Ramalho-Santos M.
Development. 140: 3624-3634

VitaminC induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.
Blaschke K, Ebata KT, Karimi MM, Zepeda-Martinez JA, Goya P, Mahapatra S, Tam A, Laird DJ, Hirst M, Rao A, Lorincz MC, Ramalho-Santos M. 
Nature. 500: 222-226

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo.
Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M.
Cell Rep. 3: 1777-1784
Smad2 Is Essential for Maintenance of the Human and Mouse Primed Pluripotent Stem Cell State.
Sakaki-Yumoto M, Liu J, Ramalho-Santos M, Yoshida N, Derynck R.
J Biol Chem. 288: 18546-18560


Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF.
PLoS Genet. 8(3):e1002576

Transcriptional analysis of pluripotency reveals the Hippo pathway as a barrier to reprogramming.
Qin H, Blaschke K, Wei G, Ohi Y, Blouin L, Qi Z, Yu J, Yeh R-F, Hebrok M, Ramalho-Santos M.
Hum Mol Genet. 21: 2054-2067


Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.
Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M.
Nat Cell Biol. 13: 541-549

Open chromatin in pluripotency and reprogramming.
Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M.
Nat Rev Mol Cell Biol. 12: 36-47


Parallel gateways to pluripotency: open chromatin in stem cells and development.
Koh FM, Sachs M, Guzman-Ayala M, Ramalho-Santos M.
Curr Opin Genet Dev. 20: 492-499


Chd1 regulates open chromatin and pluripotency of embryonic stem cells.
Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, Ramalho-Santos M.
Nature. 460: 863-868

iPS Cells: Insights into Basic Biology.
Ramalho-Santos M.
Cell. 138: 616-618


Comparative MobyDick for detection of cis-regulatory motifs.
Chaivorapol C, Melton C, Wei G, Yeh R-F, Ramalho-Santos M, Blelloch R, Li H.
BMC Bioinformatics. 9: 455

The pluripotent transcriptome.
Grskovic M, Ramalho-Santos M.
Stembook. Ed The Stem Cell Research Community, doi/10.3824/stembook.1.24.1,

High-efficiency stem cell fusion-mediated assay reveals Sall4 as an enhancer of reprogramming.
Wong C, Gaspar-Maia A, Ramalho-Santos M, Reijo Pera R.
PLoS ONE. 3(4): e1955


Generation of induced pluripotent stem cells in the absence of drug selection.
Blelloch R, Venere M, Yen J, Ramalho-Santos M.
Cell Stem Cell. 1: 245-247

Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.
Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H*, Ramalho-Santos M.
PLoS Genetics. 3: 1524-1540

On the origin of the term ‘stem cell’.
Ramalho-Santos M, Willenbring H.
Cell Stem Cell. 1: 35-38


RNA interference in embryonic stem cells and the prospects for future therapies.
Heidersbach A, Gaspar-Maia A, McManus M, Ramalho-Santos M.
Gene Therapy. 13: 478-86


Stem cells as probabilistic self-producing entities.
Ramalho-Santos M.
Bioessays. 26: 1013-6


"Stemness": transcriptional profiling of embryonic and adult stem cells.
Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA.
Science. Oct 18;298(5593):597-600


Smoothened mutants reveal redundant roles for Shh and Ihh signaling including regulation of L/R symmetry by the mouse node.
Zhang XM, Ramalho-Santos M, McMahon AP.
Cell. Jul 27;106(2):781-92


Hedgehog signals regulate multiple aspects of gastrointestinal development.
Ramalho-Santos M, Melton DA, McMahon AP.
Development. Jun;127(12):2763-72